During his DebConf15 keynote, Jacob Appelbaum observed that those listening on the Internet lines would have good reason to believe a computer have a given security hole if it download a security fix from a Debian mirror. This is a good reason to always use encrypted connections to the Debian mirror, to make sure those listening do not know which IP address to attack. In August, Richard Hartmann observed that encryption was not enough, when it was possible to interfere download size to security patches or the fact that download took place shortly after a security fix was released, and proposed to always use Tor to download packages from the Debian mirror. He was not the first to propose this, as the apt-transport-tor package by Tim Retout already existed to make it easy to convince apt to use Tor, but I was not aware of that package when I read the blog post from Richard.
Richard discussed the idea with Peter Palfrader, one of the Debian sysadmins, and he set up a Tor hidden service on one of the central Debian mirrors using the address vwakviie2ienjx6t.onion, thus making it possible to download packages directly between two tor nodes, making sure the network traffic always were encrypted.
Here is a short recipe for enabling this on your machine, by installing apt-transport-tor and replacing http and https urls with tor+http and tor+https, and using the hidden service instead of the official Debian mirror site. I recommend installing etckeeper before you start to have a history of the changes done in /etc/.
apt install apt-transport-tor sed -i 's% http://ftp.debian.org/% tor+http://vwakviie2ienjx6t.onion/%' /etc/apt/sources.list sed -i 's% http% tor+http%' /etc/apt/sources.list
If you have more sources listed in /etc/apt/sources.list.d/, run the sed commands for these too. The sed command is assuming your are using the ftp.debian.org Debian mirror. Adjust the command (or just edit the file manually) to match your mirror.
This work in Debian Jessie and later. Note that tools like apt-file only recently started using the apt transport system, and do not work with these tor+http URLs. For apt-file you need the version currently in experimental, which need a recent apt version currently only in unstable. So if you need a working apt-file, this is not for you.
Another advantage from this change is that your machine will start using Tor regularly and at fairly random intervals (every time you update the package lists or upgrade or install a new package), thus masking other Tor traffic done from the same machine. Using Tor will become normal for the machine in question.
On Freedombox, APT is set up by default to use apt-transport-tor when Tor is enabled. It would be great if it was the default on any Debian system.